X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details 100 mM Tris HCl pH 8.5, 30% PEG 400, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.24 α = 90
b = 149.97 β = 90
c = 175.78 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M K-B Focusing Mirrors 2011-12-14
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal, Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.97950 SSRL BL12-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
4.37 46.58 95.0 -- -- -- -- 22481 21374 -3.0 -3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
4.37 4.48 99.8 0.597 0.597 3.9 6.9 1636

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 4.37 37.914 -- 0.0 22481 21374 1080 94.81 0.268 0.268 0.2669 0.2881 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 4.37 4.5686 -- 132 2315 0.2945 0.3305 -- 88.0
X Ray Diffraction 4.5686 4.809 -- 141 2413 0.2576 0.3269 -- 92.0
X Ray Diffraction 4.809 5.1097 -- 136 2430 0.232 0.283 -- 93.0
X Ray Diffraction 5.1097 5.5031 -- 142 2510 0.239 0.2607 -- 95.0
X Ray Diffraction 5.5031 6.0549 -- 104 2547 0.2517 0.3058 -- 95.0
X Ray Diffraction 6.0549 6.9264 -- 132 2597 0.2569 0.3059 -- 97.0
X Ray Diffraction 6.9264 8.7091 -- 141 2701 0.2468 0.2445 -- 100.0
X Ray Diffraction 8.7091 37.9153 -- 152 2781 0.2878 0.2954 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.075
f_dihedral_angle_d 16.465
f_angle_d 1.111
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13678
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
Bluice Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
Phaser model building
Bluice data collection